Go to your mail site (google, hotmail, yahoo, etc..) and do a clean up of all the old files. Basically just to make sure you have only the most up to date ones. This should help evolution when fetching the files.

I found that worked for a while, however eventually the error comes back and does't go even if you do all of the above.

In that instance what I did was rename the Inbox (mailbox file) contained in mail/local to Inbox_old then started evolution and downloaded the new mail. So now, it wouldn't allow me to access the old Inbox mail obviously. So, in order to access the old Inbox mail, I created another folder in Evolution, but not under Inbox - at the same level.

Then I renamed the 'old' file that had been created in mail/local and copied the Inbox_old to 'old' and restarted Evolution. It complains a bit on the initial access of the 'old' folder, but then it starts rebuilding and sorts everything out.

I now have a new Inbox and all my old inbox files full accessible via the new folder 'old' from within Evolution.